Sometimes after you have enabled the “Show hidden files and folders” option in the Folder Options, the hidden files are not displayed in Windows Explorer.

Solution :

This happens if the system is infected by Virus or other Malware, which modifies the some registry values.

This is done by many Viruses, so that the hidden file (malicious executable or script) won’t be displayed in Explorer. Also note that some Viruses remove the above option altogether from the View tab of Folder Options.